Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017870.1 Corchorus olitorius cultivar O-4 contig17903, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 7490
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34


Found at i:8 original size:3 final size:3

Alignment explanation


    Indices: 1--122  Score: 226
    Period size: 3  Copynumber: 40.7  Consensus size: 3

                                                                           
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT

                                                                           
         49 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT

                              *       *       
         97 TAT TAT TAT TAT TAG TAT TAG TAT TA
          1 TAT TAT TAT TAT TAT TAT TAT TAT TA

        123 GTATATTAGT


Statistics
Matches: 115,  Mismatches: 4, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
   3  115  1.00

ACGTcount: A:0.34, C:0.00, G:0.02, T:0.65


Consensus pattern (3 bp):   
TAT

Found at i:151 original size:6 final size:6

Alignment explanation


    Indices: 142--170  Score: 58
    Period size: 6  Copynumber: 4.8  Consensus size: 6

        132 TATATTAATA

                                             
        142 TATATC TATATC TATATC TATATC TATAT
          1 TATATC TATATC TATATC TATATC TATAT

        171 TTTATCACCT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   23  1.00

ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52


Consensus pattern (6 bp):   
TATATC

Found at i:3057 original size:17 final size:18

Alignment explanation


    Indices: 3037--3071  Score: 63
    Period size: 18  Copynumber: 2.0  Consensus size: 18

       3027 TTATTATTAT

                              
       3037 TTATATTT-TATGTTTTA
          1 TTATATTTATATGTTTTA

                              
       3054 TTATATTTATATGTTTTA
          1 TTATATTTATATGTTTTA

       3072 CTTGCTTCTA


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  17    8  0.47
  18    9  0.53

ACGTcount: A:0.26, C:0.00, G:0.06, T:0.69


Consensus pattern (18 bp):   
TTATATTTATATGTTTTA

Found at i:5680 original size:17 final size:17

Alignment explanation


    Indices: 5658--5702  Score: 81
    Period size: 17  Copynumber: 2.6  Consensus size: 17

       5648 TTTCATCATC

                             
       5658 TTCACATTCACAGAATG
          1 TTCACATTCACAGAATG

                             
       5675 TTCACATTCACAGAATG
          1 TTCACATTCACAGAATG

              *        
       5692 TTAACATTCAC
          1 TTCACATTCAC

       5703 TGAGTTGTTC


Statistics
Matches: 27,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  17   27  1.00

ACGTcount: A:0.36, C:0.24, G:0.09, T:0.31


Consensus pattern (17 bp):   
TTCACATTCACAGAATG

Found at i:6915 original size:31 final size:32

Alignment explanation


    Indices: 6880--6939  Score: 86
    Period size: 31  Copynumber: 1.9  Consensus size: 32

       6870 AAAATGCCAC

                  *                         
       6880 GTGGCATTGCCACATCATCAG-TTGGTCCGAT
          1 GTGGCAATGCCACATCATCAGTTTGGTCCGAT

                        **               
       6911 GTGGCAATGCCATGTCATCAGTTTGGTCC
          1 GTGGCAATGCCACATCATCAGTTTGGTCC

       6940 AAGGTGGCGG


Statistics
Matches: 25,  Mismatches: 3, Indels: 1
        0.86            0.10        0.03

Matches are distributed among these distances:
  31   18  0.72
  32    7  0.28

ACGTcount: A:0.18, C:0.25, G:0.27, T:0.30


Consensus pattern (32 bp):   
GTGGCAATGCCACATCATCAGTTTGGTCCGAT

Found at i:6947 original size:32 final size:31

Alignment explanation


    Indices: 6880--6947  Score: 82
    Period size: 31  Copynumber: 2.2  Consensus size: 31

       6870 AAAATGCCAC

                  *                     * *
       6880 GTGGCATTGCCACATCATCAGTTGGTCCGAT
          1 GTGGCAATGCCACATCATCAGTTGGTCCAAG

                        **                  
       6911 GTGGCAATGCCATGTCATCAGTTTGGTCCAAG
          1 GTGGCAATGCCACATCATCAG-TTGGTCCAAG

                 
       6943 GTGGC
          1 GTGGC

       6948 GGCATGACGG


Statistics
Matches: 31,  Mismatches: 5, Indels: 1
        0.84            0.14        0.03

Matches are distributed among these distances:
  31   18  0.58
  32   13  0.42

ACGTcount: A:0.19, C:0.24, G:0.29, T:0.28


Consensus pattern (31 bp):   
GTGGCAATGCCACATCATCAGTTGGTCCAAG
Done.